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LOCUS	    JX446725		    5057 bp    RNA     linear	VRL 12-OCT-2012
DEFINITION  HIV-1 isolate AA005a03L from Thailand gag protein (gag) gene,
	    complete cds; pol protein (pol) gene, partial cds; and vif protein
	    (vif) and vpr protein (vpr) genes, complete cds
ACCESSION   JX446725
VERSION     JX446725.1 GI:407732208
KEYWORDS    .
SOURCE	    Human immunodeficiency virus 1 (HIV-1)
  ORGANISM  Human immunodeficiency virus 1 Viruses; Retro-transcribing viruses;
	    Retroviridae; Orthoretrovirinae; Lentivirus; Primate lentivirus
	    group
REFERENCE   1 (bases 1 to 5057)
            Show all sequences for reference 1
  AUTHORS   Rolland,M., Edlefsen,P.T., Larsen,B.B., Tovanabutra,S.,
	    Sanders-Buell,E., Hertz,T., deCamp,A.C., Carrico,C., Menis,S.,
	    Magaret,C.A., Ahmed,H., Juraska,M., Chen,L., Konopa,P., Nariya,S.,
	    Stoddard,J.N., Wong,K., Zhao,H., Deng,W., Maust,B.S., Bose,M.,
	    Howell,S., Bates,A., Lazzaro,M., O'Sullivan,A., Lei,E.,
	    Bradfield,A., Ibitamuno,G., Assawadarachai,V., O'Connell,R.J.,
	    deSouza,M.S., Nitayaphan,S., RERKS-NGARM,S., Robb,M.L.,
	    McLellan,J.S., Georgiev,I., Kwong,P.D., Carlson,J.M., Michael,N.L.,
	    Schief,W.R., Gilbert,P.B., Mullins,J.I. and Kim,J.H.
  TITLE     Increased HIV-1 vaccine efficacy against viruses with genetic
	    signatures in Env V2.
  JOURNAL   Nature.. 490(7420); 417-20 (2012)
  PUBMED    22960785
REFERENCE   2 (bases 1 to 5057)
            Show all sequences for reference 2
  AUTHORS   Rolland,M., Edlefsen,P.T., Larsen,B.B., Tovanabutra,S.,
	    Sanders-Buell,E., Hertz,T., de Camp,A.C., Carrico,C., Menis,S.,
	    Magaret,C.A., Ahmed,H., Juraska,M., Chen,L., Konopa,P., Nariya,S.,
	    Stoddard,J.N., Wong,K., Zhao,H., Deng,W., Maust,B.S., Bose,M.,
	    Howell,S., Bates,A., Lazzaro,M., O'Sullivan,A., Lei,E.,
	    Bradfield,A., Ibitamuno,G., Assawadarachai,V., O'Connell,R.J., de
	    Souza,M.S., Nitayaphan,S., RERKS-NGARM,S., Robb,M.L.,
	    McLellan,J.S., Georgiev,I., Kwong,P.D., Carlson,J.M., Michael,N.L.,
	    Schief,W.R., Gilbert,P.B., Mullins,J.I. and Kim,J.H.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-AUG-2012) US Military HIV Research Program, 503
	    Robert Grant Ave, Silver Spring, MD 20910, USA
COMMENT     ##Assembly-Data-START## Sequencing Technology Sanger dideoxy
	    sequencing ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source	     1..5057
		     /organism="Human immunodeficiency virus 1"
		     /mol_type="genomic RNA"
		     /isolate="AA005a03L"
		     /isolation_source="plasma AA005a"
		     /host="Homo sapiens; RV144 trial participant AA005"
		     /db_xref="taxon:11676"
		     /country="Thailand"
		     /collection_date="2007"
		     /note="subtype: CRF01_AE"
     gene	     2..1498
		     /gene="gag"
     CDS	     2..1498
		     /gene="gag"
		     /codon_start="1"
		     /transl_table="1"
		     /product="gag protein"
		     /protein_id="AFU26148.1"
		     /db_xref="GI:407732209"
		     /translation="MGARASVLTGGKLDAWEKIRLRPGGKKKYRIKHLVWASRELERF
		     ALNPGLLETSEGCQQIIEQLQSTLKTGSEELKSLYNAVATLWCVHQRIDVKDTKEALD
		     KMEEAQKRSQQKTQQAAAGTGSSSKVSQNYPIVQNAQGQMVHQSLSPRTLNAWVKVVE
		     EKGFNPEVIPMFSALSEGATPQDLNMMLNIVGGHQAAMQMLKETINEEAAEWDRVHPV
		     HAGPIPPGQMREPRGSDIAGTTSTLQEQIGWMTSNPPIPVGDIYKRWIILGLNKIVRM
		     YSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNANPDCKSIL
		     KALGTGATLEEMMTACQGVGGPSHKARVLAEAMSQAQNVNIMMQRGNFKGQKRIKCFN
		     CGKEGHLARNCRAPRKRGCWKCGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFPQSR
		     PEPSAPPAENWGMGEETPSLLKQEQKDREHPPPSVSLKSLFGNDPLSQ"
     misc_feature    5..>334
		     /gene="gag"
		     /note="gag gene protein p17 (matrix protein); Region:
		     Gag_p17; pfam00540"
		     /db_xref="CDD:109591"
     misc_feature    446..1090
		     /gene="gag"
		     /note="gag gene protein p24 (core nucleocapsid protein);
		     Region: Gag_p24; pfam00607"
		     /db_xref="CDD:201337"
     misc_feature    1163..1216
		     /gene="gag"
		     /note="Zinc knuckle; Region: zf-CCHC; pfam00098"
		     /db_xref="CDD:189387"
     misc_feature    1226..1279
		     /gene="gag"
		     /note="Zinc knuckle; Region: zf-CCHC; pfam00098"
		     /db_xref="CDD:189387"
     misc_feature    1340..1447
		     /gene="gag"
		     /note="Gag protein p6; Region: Gag_p6; pfam08705"
		     /db_xref="CDD:149684"
     gene	     <1291..4302
		     /gene="pol"
     CDS	     <1291..4302
		     /gene="pol"
		     /codon_start="1"
		     /transl_table="1"
		     /product="pol protein"
		     /protein_id="AFU26149.1"
		     /db_xref="GI:407732210"
		     /translation="FFRENLAFQQRKAREFSSEQTRAISPTSRKLGDGGRDTFLAEAG
		     AERQGTPSSFSFPQITLWQRPLVTVKIGGQLREALLDTGADDTVLEEINLPGKWKPKM
		     IGGIGGFIKVRQYDQILIEICGKKAIGTVLVGPTPVNIIGRNMLTQIGCTLNFPISPI
		     DTVPVTLKPGMDGPKVKQWPLTEEKIKALTEICKEMEEEGKISKIGPENPYNTPIFAI
		     KKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLD
		     ESFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRIKNPEIV
		     IYQYMDDLYVGSDLEIGQHRTKVEELRAHLLSWGFTTPDKKHQKEPPFLWMGYELHPD
		     KWTVQPIELPEKDSWTVNDIQKLVGKLNWASQIYPGIKVKQLCRLLRGAKALTDIVPL
		     TEEAELELAENREILKTPVHGVYYDPSKDLIAEVQKQGQDQWTYQIYQEPFKNLKTGK
		     YARKRSTHTNDVRQLAEAVQKIATESIVIWGKTPKFKLPIQRETWETWWMEYWQATWI
		     PEWEFVNTPPLVKLWYQLEKDPIVGAETFYVDGAASRETKLGKAGYVTDRGRQKVVSL
		     TETTNQKTELQAIHLALQDSGSEVNIVTDSQYALGIIQAQPDRSESEVVNQIIEDLIK
		     KEKVYLSWVPAHKGIGGNEQVDKLVSSGIRKVLFLDGIDKAQEEHERYHSNWRTMASD
		     FNLPPIVAKEIVASCDKCQLKGEALHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGY
		     IEAEVIPAETGHETAYFLLKLAGRWPVKVVHTDNGSNFTSAAVKAACWWANIKQEFGI
		     PYNPQSQGVVESMNKELKKIIGQIRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGER
		     IIDIIATDIQTKELQKQITKIQNFRVYYRDSRDPIWKGPAKLLWKGEGAVVIQDNSDI
		     KVVPRRKAKIIRDYGKQMAGDDCVAGRQDED"
     misc_feature    1489..1731
		     /gene="pol"
		     /note="Retropepsins, pepsin-like aspartate proteases;
		     Region: HIV_retropepsin_like; cd05482"
		     /db_xref="CDD:133149"
     misc_feature    order(1531..1533,1537..1539,1543..1545,1594..1602,1708..17
		     10)
		     /gene="pol"
		     /note="inhibitor binding site; inhibition site"
		     /db_xref="CDD:133149"
     misc_feature    1531..1539
		     /gene="pol"
		     /note="catalytic motif [active]"
		     /db_xref="CDD:133149"
     misc_feature    1531..1533
		     /gene="pol"
		     /note="Catalytic residue [active]"
		     /db_xref="CDD:133149"
     misc_feature    order(1594..1608,1612..1626)
		     /gene="pol"
		     /note="Active site flap [active]"
		     /db_xref="CDD:133149"
     misc_feature    1807..2457
		     /gene="pol"
		     /note="RT_Rtv: Reverse transcriptases (RTs) from
		     retroviruses (Rtvs). RTs catalyze the conversion of
		     single-stranded RNA into double-stranded viral DNA for
		     integration into host chromosomes. Proteins in this
		     subfamily contain long terminal repeats (LTRs) and...;
		     Region: RT_Rtv; cd01645"
		     /db_xref="CDD:73152"
     misc_feature    order(1825..1830,1936..1938,1948..1950,1969..1971,1975..19
		     83,1987..1989,1996..1998,2020..2022,2026..2031,2035..2037,
		     2083..2100,2206..2211,2215..2217,2224..2226,2302..2304,230
		     8..2313,2443..2448)
		     /gene="pol"
		     /note="active site"
		     /db_xref="CDD:73152"
     misc_feature    order(1825..1830,1975..1983,1987..1989,1996..1998,2020..20
		     22,2026..2031,2035..2037,2209..2211,2215..2217,2224..2226,
		     2302..2304,2443..2448)
		     /gene="pol"
		     /note="DNA binding site [nucleotide binding]"
		     /db_xref="CDD:73152"
     misc_feature    1942..2457
		     /gene="pol"
		     /note="Reverse transcriptase (RNA-dependent DNA
		     polymerase); Region: RVT_1; pfam00078"
		     /db_xref="CDD:200982"
     misc_feature    order(1948..1950,1969..1971,2083..2100,2206..2208,2308..23
		     10)
		     /gene="pol"
		     /note="dNTP binding site [chemical binding]; other site"
		     /db_xref="CDD:73152"
     misc_feature    order(2053..2064,2290..2292,2296..2298,2317..2319,2323..23
		     25,2434..2436)
		     /gene="pol"
		     /note="NNRTI binding site; other site"
		     /db_xref="CDD:73152"
     misc_feature    2467..2676
		     /gene="pol"
		     /note="Reverse transcriptase thumb domain; Region:
		     RVT_thumb; pfam06817"
		     /db_xref="CDD:115473"
     misc_feature    2704..3012
		     /gene="pol"
		     /note="Reverse transcriptase connection domain; Region:
		     RVT_connect; pfam06815"
		     /db_xref="CDD:203523"
     misc_feature    3070..3408
		     /gene="pol"
		     /note="non-LTR RNase HI domain of reverse transcriptases;
		     Region: Rnase_HI_RT_non_LTR; cd09276"
		     /db_xref="CDD:187700"
     misc_feature    order(3082..3084,3187..3189,3247..3249,3400..3402)
		     /gene="pol"
		     /note="active site"
		     /db_xref="CDD:187700"
     misc_feature    order(3082..3090,3094..3096,3172..3180,3187..3189,3247..32
		     49,3358..3360)
		     /gene="pol"
		     /note="RNA/DNA hybrid binding site [nucleotide binding];
		     other site"
		     /db_xref="CDD:187700"
     misc_feature    3457..3576
		     /gene="pol"
		     /note="Integrase Zinc binding domain; Region:
		     Integrase_Zn; pfam02022"
		     /db_xref="CDD:202092"
     misc_feature    3607..3921
		     /gene="pol"
		     /note="Integrase core domain; Region: rve; pfam00665"
		     /db_xref="CDD:201381"
     misc_feature    4093..4245
		     /gene="pol"
		     /note="Integrase DNA binding domain; Region: IN_DBD_C;
		     pfam00552"
		     /db_xref="CDD:144223"
     gene	     4247..4825
		     /gene="vif"
     CDS	     4247..4825
		     /gene="vif"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vif protein"
		     /protein_id="AFU26150.1"
		     /db_xref="GI:407732211"
		     /translation="MENRWQVMIVWQVDRMRIRTWHSLVKYHMYVSKKAKNWFYRHHY
		     ESQHPKVSSEVHIPIGEARLVVRTYWGLQTGEKAWQLGHGVSIEWRQGKYNTQVDPDL
		     ADQLIHLQYFDCFSDSAIRKAILGQVVRHRCEYPSGHNKVGSLQYLALKALTAPKRIK
		     PPLPSVKKLTEDRWNKPQKIRGHRENPTMNGH"
     misc_feature    4247..4822
		     /gene="vif"
		     /note="Retroviral Vif (Viral infectivity) protein; Region:
		     Vif; pfam00559"
		     /db_xref="CDD:109609"
     gene	     4765..5055
		     /gene="vpr"
     CDS	     4765..5055
		     /gene="vpr"
		     /codon_start="1"
		     /transl_table="1"
		     /product="vpr protein"
		     /protein_id="AFU26151.1"
		     /db_xref="GI:407732212"
		     /translation="MEQAPEDQGPQREPYNEWTLELLEELKNEAVRHFPRPWLHGLGQ
		     HIYNTYGDTWEGVEAIVRILHQLLFVHFRIGCQHSRIGIIPGRRGRNGAGRS"
     misc_feature    4765..5001
		     /gene="vpr"
		     /note="VPR/VPX protein; Region: VPR; pfam00522"
		     /db_xref="CDD:109573"
BASE COUNT     1926 a	 865 c	 1191 g   1075 t
ORIGIN
       1 gatgggtgcg agagcgtcag tattaactgg gggaaaatta gatgcatggg aaaaaattcg 
      61 gttgcggcca gggggaaaga aaaaatatag gataaaacat ttagtatggg caagcagaga 
     121 gttagaaaga tttgcactta accctggcct tttagaaaca tcagaaggat gtcaacagat 
     181 aatagaacag ttacaatcaa ctctcaagac aggatcagag gaacttaaat ctttatataa 
     241 tgcagtagca accctttggt gcgtacacca aagaatagat gtaaaagaca ccaaggaagc 
     301 tttagataaa atggaagaag cacaaaagag gagtcagcaa aagacacaac aggcagcagc 
     361 tggcacagga agcagcagca aagtcagcca aaattaccct atagtgcaaa atgcacaagg 
     421 gcaaatggta catcagtctt tatcacctag aactttgaat gcatgggtaa aagtagtaga 
     481 agaaaagggt tttaaccctg aagtaatacc catgttctca gcattatcag agggagccac 
     541 cccacaagat ttaaatatga tgctaaatat agtgggagga caccaggcag caatgcaaat 
     601 gttaaaagaa accatcaatg aggaagctgc agaatgggat agggtacacc cagtacatgc 
     661 agggccgatt ccaccaggcc agatgaggga accaagggga agtgacatag caggaactac 
     721 tagtaccctt caagaacaaa taggatggat gacaagcaat ccacctatcc cagtgggaga 
     781 tatctataaa aggtggataa tcctgggatt aaataaaata gtaagaatgt atagccctgt 
     841 tagcattttg gacataagac aagggccaaa agaacccttc agagactatg tagataggtt 
     901 ctataagact ctcagagcag aacaagctac acaggaggta aagaattgga tgacagaaac 
     961 cttgctagtc caaaatgcga atccagactg taaatccatc ttaaaagcat taggaacagg 
    1021 agctacatta gaagagatga tgacagcatg tcagggagtg ggaggaccta gccataaagc 
    1081 aagggttttg gctgaggcaa tgagccaagc acaaaatgta aatataatga tgcagagagg 
    1141 caactttaag ggccagaaaa gaattaagtg cttcaactgt ggcaaagaag ggcacctagc 
    1201 cagaaattgc agggccccta gaaaaagggg ttgttggaaa tgtggaaagg aaggacatca 
    1261 aatgaaagac tgcactgaga gacaggctaa ttttttaggg aaaatctggc cttccaacaa 
    1321 aggaaggcca gggaattttc ctcagagcag accagagcca tcagccccac cagcagaaaa 
    1381 ctgggggatg ggggaagaga caccttcctt gctgaagcag gagcagaaag acagggaaca 
    1441 ccctcctcct tcagtttccc tcaaatcact ctttggcaac gaccccttgt cacagtaaaa 
    1501 ataggaggac aactaagaga agctctatta gatacaggag cagatgatac agtattagaa 
    1561 gaaataaatt tgccaggaaa atggaaacca aaaatgatag ggggaattgg aggttttatc 
    1621 aaagtaaggc aatatgatca gatacttata gaaatttgtg gaaagaaggc tataggtaca 
    1681 gtgttagtag gacctacacc tgtcaacata attggacgaa atatgttgac tcagattggc 
    1741 tgtactttaa atttcccaat tagtcctatt gacactgtac cagtaacatt aaagccagga 
    1801 atggatggac caaaggttaa acaatggcca ttgacagaag aaaaaataaa agcattaaca 
    1861 gaaatttgta aagagatgga agaggaagga aaaatctcaa aaattgggcc tgaaaatcca 
    1921 tacaatactc caatatttgc tataaagaaa aaggacagca ccaagtggag gaaattagta 
    1981 gatttcagag agctcaataa aagaacacag gacttttggg aagttcaatt aggaatacca 
    2041 catccagcag gtttaaaaaa gaaaaaatca gtgacagtac tagatgtggg agatgcatat 
    2101 ttttcagttc ctttagatga aagctttaga aagtatactg catttaccat acctagtata 
    2161 aacaatgaaa caccaggaat tagatatcag tacaatgtgc tgccacaggg atggaaagga 
    2221 tcaccggcaa tattccagag tagcatgaca aaaatcttag agccctttag aataaaaaat 
    2281 ccagaaatag ttatctatca atacatggat gacttgtatg taggatctga tttagaaata 
    2341 gggcagcaca gaacaaaagt agaggagcta agagctcatc tattgagctg gggatttact 
    2401 acaccagaca aaaagcatca gaaggaacct ccattccttt ggatggggta tgagctccat 
    2461 cctgacaaat ggacagtcca gcctatagaa ctgccagaaa aagacagctg gactgtcaat 
    2521 gatatacaga aattagtggg aaagctaaat tgggcaagtc aaatttatcc agggattaag 
    2581 gtaaagcaac tgtgtagact cctcagggga gctaaagcac taacagacat agtaccactg 
    2641 actgaagaag cagaattaga attagcagag aacagggaga ttctaaaaac ccctgtgcat 
    2701 ggggtatatt atgacccatc aaaagactta atagcagaag tacagaaaca agggcaagac 
    2761 caatggacat atcaaattta tcaggagcca tttaaaaatc taaagacagg aaaatatgca 
    2821 agaaaaaggt ctactcacac taatgatgta agacaattag cagaagcggt gcaaaaaata 
    2881 gccacagaga gcatagtaat atggggaaag acccctaaat ttaaattgcc catacaaaga 
    2941 gagacatggg aaacatggtg gatggagtat tggcaagcta cctggattcc tgaatgggag 
    3001 tttgtcaata cccctcctct agtaaaatta tggtatcaat tagaaaagga ccccatagta 
    3061 ggagcagaga ctttctatgt agatggggca gctagtaggg agactaagct aggaaaagca 
    3121 ggatatgtca ctgacagagg aagacaaaag gtagtttccc taactgagac aacaaatcaa 
    3181 aagactgaat tacaagcgat ccatttagcc ttgcaggatt caggatcaga agtaaatata 
    3241 gtaacagact cacaatatgc attaggaatc attcaggcgc aaccagacag gagtgaatca 
    3301 gaagtagtca accaaataat agaggactta ataaaaaagg aaaaggtcta cctgtcatgg 
    3361 gtaccagcac acaaagggat tggaggaaat gaacaagtag ataaattagt cagttcagga 
    3421 atcaggaagg tgctcttttt agatggcata gataaggctc aagaagagca tgaaagatat 
    3481 cacagcaatt ggagaacaat ggctagtgat tttaatttgc cacctatagt agcaaaggag 
    3541 atagtagcca gctgtgataa atgtcagcta aaaggggaag ctctacatgg acaagtggac 
    3601 tgtagtccag gaatatggca attagattgc acacacctag aagggaaagt catcctggta 
    3661 gcagtccacg tggccagtgg atatatagaa gcagaagtta tcccagcaga aacagggcat 
    3721 gagacagcat actttctgct aaaattagca ggaagatggc cagtaaaagt agtacacact 
    3781 gacaatggta gcaatttcac cagcgctgca gttaaagcag cctgttggtg ggccaatatc 
    3841 aaacaggaat ttgggattcc ctacaatccc caaagtcaag gagtagtaga gtctatgaat 
    3901 aaagaattaa agaaaatcat aggacagata agagatcaag ctgaacatct taagacagca 
    3961 gtacaaatgg cagtattcat tcacaatttt aaaagaaaag gggggattgg ggggtacagt 
    4021 gcaggggaaa gaataataga cataatagca acagacatac aaactaaaga actacaaaaa 
    4081 caaattacaa aaattcaaaa ttttcgggtt tattacaggg acagcagaga cccaatttgg 
    4141 aaaggaccag caaaactact ctggaaaggt gaaggggcag tagtaataca agacaatagt 
    4201 gatatcaaag tagtaccaag aagaaaagca aagatcatta gggattatgg aaaacagatg 
    4261 gcaggtgatg attgtgtggc aggtagacag gatgaggatt agaacatggc acagtttagt 
    4321 aaaatatcat atgtatgtct caaagaaagc taaaaattgg ttttatagac atcattatga 
    4381 aagccagcat ccaaaagtaa gttcagaagt acatatccca ataggagagg ccagattagt 
    4441 agtgagaaca tattggggtc tgcagacagg agaaaaggca tggcaattgg gtcatggagt 
    4501 ctccatagaa tggaggcagg gaaaatataa cacacaagtc gatcctgacc tagcagacca 
    4561 actgattcat ctacaatatt ttgactgttt ttcagactct gccataagga aagccatatt 
    4621 aggacaagta gttagacata ggtgtgaata tccatcagga cataataagg taggatccct 
    4681 acaatatttg gcactgaaag cattaacagc accaaaaagg ataaagccac ctctgcccag 
    4741 tgttaagaaa ttaacagaag atagatggaa caagccccag aagatcaggg gccacagaga 
    4801 gaaccctaca atgaatggac attagaactg ttagaggagc ttaaaaatga agctgttaga 
    4861 cattttccca gaccctggct ccatggctta ggacagcaca tttataacac ttatggggat 
    4921 acttgggaag gggttgaagc tatagtaaga atcttgcatc aactgctgtt tgttcatttc 
    4981 agaattgggt gtcaacatag cagaataggc attataccag ggagaagagg caggaatgga 
    5041 gccggtagat cctaacc
//
last modified: Tue May 31 10:56 2022


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